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Annotum: an open-source journal authoring and publishing platform based on WordPress

Introduction and Background

[Author's Note 31-Jan-2012: For updated information please see http://annotum.org, and for a much more recent paper on the same subject, please see: http://www.ncbi.nlm.nih.gov/books/NBK63828/]

Despite significant advances in most forms of publishing, from blogs to news sites and other user-generated web content, the process of authoring scholarly articles remains an expensive, time-consuming process that can require significant up-front investment and technical expertise.  While a number of electronic publishing and workflow management systems exist, those intended for the scientific publishing (SP) community  provide at best only rudimentary authoring tools – and in many cases merely provide a repository for document files created in other formats, with no authoring features at all.  It is as if the entire revolution in online, web-based content authoring tools has passed the SP community by.  And despite the development of advanced document formats such as the National Library of Medicine’s (NLM) journal article document type definition (DTD), virtually no current system allows scientific authors to easily create structured documents based on the DTD by using simple web-based tools.

Annotum, a new open-source journal authoring and publishing system being developed by Solvitor LLC (with private funding), will fill the void in web-based authoring tools for the SP community.  Annotum will be released as open-source software, freely available to anyone in the SP community to use, extend, or enhance.  Hosted versions of Annotum will also be available for a moderate hosting fee -- in line with blog hosting services currently available.

Project Objective

Develop a simple, robust, easy-to-use authoring system to create and edit scholarly articles using the NLM Journal article DTD format, and deliver a working, functional system that can be used to create, maintain, and publish scholarly articles.

Project Approach

Modern platforms such as WordPress provide a model for a successful eJournal authoring platform – WordPress is extremely simple to set up and run, with rich, user-friendly web-based editing controls and easily-extended functionality using plugins.  The WordPress ‘ecosystem’ not only provides free and open access to source code, with a rich array of developers for themes, plugins, and extensions, but also numerous cheap or free hosting opportunities for technical and non-technical users alike.

However, WordPress is missing some key SP requirements:

  • Support for multiple authors, article review workflow, and version comparison
  • Scholarly features such as citations, equations, and controlled document structure (headings, lists of figures/equations/tables)
  • Export to and import from the NLM/PubMed Journal Article DTD and other structured formats
  • Strict enforcement of document structure to ensure DTD conformance
Annotum will build upon the WordPress platform as a foundation, filling in the gaps by providing the following additional features:
  • Rich, web-based scholarly article authoring and editing:
    • “What you see is what you get” (WYSIWYG) authoring with rich toolset (equations, figures, tables, citations and references)
    • coauthoring, comments, version tracking, and revision comparisons
  • Strict conformance to the appropriate DTD (e.g. NLM/PMC)
  • Multiple import and export formats
    • Export to PDF, HTML, RTF, or specified XML formats
    • Import XML formats for “round-tripping” of content
    • Articles can be cited, exported, imported across systems/sites
  • Simple editorial workflow for authoring and reviewer/editor approval
  • A set of rich, visually beautiful templates for publishing online journals

This proposed feature set is only a starting point, however.  By presenting this project overview at Beyond The PDF, I hope to gather input from science practitioners, journal publishers, tool makers, and other interested parties in order to refine and improve the requirements for Annotum version 1.0.  I also hope to generate ideas for future versions and enhancements of this open-process, open-access, open-source toolset.
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